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Posted to dev@ctakes.apache.org by "Masanz, James J." <Ma...@mayo.edu> on 2015/05/03 13:59:53 UTC
RE: What is the correct way to enable cTakes to recognize and annotate
mentions of medical devices?
I think the 'right way' would be to create a subtype of org.apache.ctakes.typesystem.type.textsem.EntityMention (rather than what you tried with a subtype of IdentifiedAnnotation)
I don't know where all the required changes would be beyond that.
If you get that to work, please create a JIRA with the information so the documentation can be updated.
If I just wanted to get it to work, I would look at one of these options
- use the method you tried with EntityMention, and if you want to get just the devices, loop through all EntityMention and check explicitly if the type is EntityMention (and not a subtype of EntityMention)
- use the method you tried with either ProcedureMention or EntityMention, and then in cases where you needed to know if it was a device, use the _ref_ontologyConceptArr to find out the TUI associated with the annotation.
Regards,
James
-----Original Message-----
From: Bruce Tietjen [mailto:bruce.tietjen@perfectsearchcorp.com]
Sent: Thursday, April 30, 2015 3:39 PM
To: dev@ctakes.apache.org
Subject: What is the correct way to enable cTakes to recognize and annotate mentions of medical devices?
Hi,
I am using the cTakes 3.2.0 code base and I have been trying to figure out
what would be the proper way to get cTakes to recognize and annotate
mentions of medical devices.
I am using the AggregatePlaintextUMLSProcessor.xml because one of the main
requirements for the annotation is that it needs to to include subject, and
polarity, certainty, etc.
First, I added TUI T074 to the procedureTuis in the LookupDesc_Db.xml. The
output from this provides mostly what I want, except it lumps the devices
as ProcedureMention where I would like them to be distinguished by their
own annotation.
An example annotation created this way was:
<org.apache.ctakes.typesystem.type.textsem.ProcedureMention
_indexed="1" _id="35574" _ref_sofa="3" begin="472" end="481" id="32"
_ref_ontologyConceptArr="35569" typeID="8" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="1.0" polarity="1" uncertainty="0"
conditional="false" generic="false" subject="patient" historyOf="0"/>
I also tried adding code to classify devices as an EntityMention, and that
seemed to work too:
<org.apache.ctakes.typesystem.type.textsem.EntityMention _indexed="1"
_id="35574" _ref_sofa="3" begin="472" end="481" id="32"
_ref_ontologyConceptArr="35569" typeID="8" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="1.0" polarity="1" uncertainty="0"
conditional="false" generic="false" subject="patient" historyOf="0"/>
Again, that doesn't give devices their own unique annotation so I looked
further. Exploring the typesystem, I noticed the following types in
TypeSystem.xml:
org.apache.ctakes.typesystem.type.refsem.ProcedureDevice
org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier
These seemed like the closest defined types to what I would expect so I
thought I would see if using them would generate what I wanted. I modified
the code to generate these annotations and the result was as follows:
<org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier
_indexed="1" _id="35587" _ref_sofa="3" begin="472" end="481" id="32"
typeID="0" segmentID="SIMPLE_SEGMENT" discoveryTechnique="0"
confidence="0.0" polarity="0" uncertainty="0" conditional="false"
generic="false" subject="patient" historyOf="0"
_ref_normalizedForm="35574"/>
<org.apache.ctakes.typesystem.type.refsem.ProcedureDevice _id="35574"
id="0" _ref_ontologyConcept="35542" discoveryTechnique="1" confidence="0.0"
conditional="false" generic="false" polarity="0" uncertainty="0"
historyOf="0"/>
The problem with this approach was that confidence, polarity, and
uncertainty did not get filled in. I tried adding these to the inputs and
outputs of the AssertionMiniPipelineAnalysisEngine, but that didn't seem to
have any effect. Perhaps I didn't do it right? or maybe it isn't even the
right pipeline component to try to modify?
Since ProcedureDevice and ProcedureDeviceModifer have different supertypes
than ProcedureMention, I also tried creating a new type in
TypeSystem.xml:
<typeDescription>
<name>org.apache.ctakes.typesystem.type.textsem.DeviceMention</name>
<supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</supertypeName>
<features>
<featureDescription>
<name>entity</name>
<description/>
<rangeTypeName>org.apache.ctakes.typesystem.type.refsem.Entity</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
Modifying the code to create this type, the result was:
<org.apache.ctakes.typesystem.type.textsem.DeviceMention _indexed="1"
_id="35574" _ref_sofa="3" begin="472" end="481" id="32"
_ref_ontologyConceptArr="35569" typeID="8" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0"
conditional="false" generic="false" subject="patient" historyOf="0"/>
Again the problem here is that confidence, polarity and uncertainty are not
filled in.
So, I am left wondering:
1) Which of the methods I tried would be the best "cTakes way"?
2) What do I need to modify to get confidence, polarity and uncertainty to
be filled in?
Thanks,
Bruce
Re: What is the correct way to enable cTakes to recognize and
annotate mentions of medical devices?
Posted by Bruce Tietjen <br...@perfectsearchcorp.com>.
James,
Thanks for the assistance.
Adding a DeviceMention that uses EntityMention as the supertype worked.
As you requested, I create JIRA 357: Adding support for mention of Medical
Devices: https://issues.apache.org/jira/browse/CTAKES-357
Thanks,
Bruce
On Sun, May 3, 2015 at 5:59 AM, Masanz, James J. <Ma...@mayo.edu>
wrote:
> I think the 'right way' would be to create a subtype of
> org.apache.ctakes.typesystem.type.textsem.EntityMention (rather than what
> you tried with a subtype of IdentifiedAnnotation)
> I don't know where all the required changes would be beyond that.
>
> If you get that to work, please create a JIRA with the information so the
> documentation can be updated.
>
> If I just wanted to get it to work, I would look at one of these options
> - use the method you tried with EntityMention, and if you want to get
> just the devices, loop through all EntityMention and check explicitly if
> the type is EntityMention (and not a subtype of EntityMention)
> - use the method you tried with either ProcedureMention or EntityMention,
> and then in cases where you needed to know if it was a device, use the
> _ref_ontologyConceptArr to find out the TUI associated with the annotation.
>
>
> Regards,
> James
>
> -----Original Message-----
> From: Bruce Tietjen [mailto:bruce.tietjen@perfectsearchcorp.com]
> Sent: Thursday, April 30, 2015 3:39 PM
> To: dev@ctakes.apache.org
> Subject: What is the correct way to enable cTakes to recognize and
> annotate mentions of medical devices?
>
> Hi,
> I am using the cTakes 3.2.0 code base and I have been trying to figure out
> what would be the proper way to get cTakes to recognize and annotate
> mentions of medical devices.
>
> I am using the AggregatePlaintextUMLSProcessor.xml because one of the main
> requirements for the annotation is that it needs to to include subject, and
> polarity, certainty, etc.
>
> First, I added TUI T074 to the procedureTuis in the LookupDesc_Db.xml. The
> output from this provides mostly what I want, except it lumps the devices
> as ProcedureMention where I would like them to be distinguished by their
> own annotation.
>
> An example annotation created this way was:
> <org.apache.ctakes.typesystem.type.textsem.ProcedureMention
> _indexed="1" _id="35574" _ref_sofa="3" begin="472" end="481" id="32"
> _ref_ontologyConceptArr="35569" typeID="8" segmentID="SIMPLE_SEGMENT"
> discoveryTechnique="1" confidence="1.0" polarity="1" uncertainty="0"
> conditional="false" generic="false" subject="patient" historyOf="0"/>
>
> I also tried adding code to classify devices as an EntityMention, and that
> seemed to work too:
> <org.apache.ctakes.typesystem.type.textsem.EntityMention _indexed="1"
> _id="35574" _ref_sofa="3" begin="472" end="481" id="32"
> _ref_ontologyConceptArr="35569" typeID="8" segmentID="SIMPLE_SEGMENT"
> discoveryTechnique="1" confidence="1.0" polarity="1" uncertainty="0"
> conditional="false" generic="false" subject="patient" historyOf="0"/>
>
> Again, that doesn't give devices their own unique annotation so I looked
> further. Exploring the typesystem, I noticed the following types in
> TypeSystem.xml:
> org.apache.ctakes.typesystem.type.refsem.ProcedureDevice
> org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier
>
> These seemed like the closest defined types to what I would expect so I
> thought I would see if using them would generate what I wanted. I modified
> the code to generate these annotations and the result was as follows:
> <org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier
> _indexed="1" _id="35587" _ref_sofa="3" begin="472" end="481" id="32"
> typeID="0" segmentID="SIMPLE_SEGMENT" discoveryTechnique="0"
> confidence="0.0" polarity="0" uncertainty="0" conditional="false"
> generic="false" subject="patient" historyOf="0"
> _ref_normalizedForm="35574"/>
> <org.apache.ctakes.typesystem.type.refsem.ProcedureDevice _id="35574"
> id="0" _ref_ontologyConcept="35542" discoveryTechnique="1" confidence="0.0"
> conditional="false" generic="false" polarity="0" uncertainty="0"
> historyOf="0"/>
>
> The problem with this approach was that confidence, polarity, and
> uncertainty did not get filled in. I tried adding these to the inputs and
> outputs of the AssertionMiniPipelineAnalysisEngine, but that didn't seem to
> have any effect. Perhaps I didn't do it right? or maybe it isn't even the
> right pipeline component to try to modify?
>
> Since ProcedureDevice and ProcedureDeviceModifer have different supertypes
> than ProcedureMention, I also tried creating a new type in
> TypeSystem.xml:
> <typeDescription>
> <name>org.apache.ctakes.typesystem.type.textsem.DeviceMention</name>
>
>
> <supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</supertypeName>
> <features>
> <featureDescription>
> <name>entity</name>
> <description/>
>
>
> <rangeTypeName>org.apache.ctakes.typesystem.type.refsem.Entity</rangeTypeName>
> </featureDescription>
> </features>
> </typeDescription>
>
> Modifying the code to create this type, the result was:
> <org.apache.ctakes.typesystem.type.textsem.DeviceMention _indexed="1"
> _id="35574" _ref_sofa="3" begin="472" end="481" id="32"
> _ref_ontologyConceptArr="35569" typeID="8" segmentID="SIMPLE_SEGMENT"
> discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0"
> conditional="false" generic="false" subject="patient" historyOf="0"/>
>
> Again the problem here is that confidence, polarity and uncertainty are not
> filled in.
>
> So, I am left wondering:
> 1) Which of the methods I tried would be the best "cTakes way"?
> 2) What do I need to modify to get confidence, polarity and uncertainty to
> be filled in?
>
> Thanks,
> Bruce
>